Showing : microbiome • reset
6
votes
1
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3.3k
views
Using R package 'limma' on pre-normalized counts and the effect of non-equivalent reads/sample on limma linear model
limma rna-seq multi-mapped reads normalization microbiome
updated 7.6 years ago by ★ 13k • written 7.6 years ago by ▴ 20
4
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3
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2.0k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 7.9 years ago by 42k • written 7.9 years ago by • 0
3
votes
2
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3.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.7 years ago by 42k • written 6.7 years ago by • 0
2
votes
2
replies
1.6k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
9.3 years ago noelle.noyes ▴ 30
2
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2
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1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
9.3 years ago noelle.noyes ▴ 30
2
votes
4
replies
2.3k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 17 months ago by • 0 • written 9.3 years ago by ▴ 30
2
votes
1
reply
1.7k
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 2.1 years ago by 42k • written 2.1 years ago by ▴ 10
2
votes
1
reply
1.8k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 8.7 years ago by 42k • written 8.7 years ago by • 0
2
votes
1
reply
1.1k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 5.5 years ago by ★ 3.6k • written 5.5 years ago by ▴ 850
2
votes
1
reply
1.1k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 8 months ago by ★ 4.1k • written 8 months ago by ▴ 10
2
votes
19
replies
2.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome DESeq Microbiome DESeq
updated 10.1 years ago by 42k • written 10.1 years ago by ▴ 130
1
vote
1
reply
1.4k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 6.5 years ago by 42k • written 6.5 years ago by • 0
1
vote
2
replies
1.9k
views
Normalization factors in metagenomeSeq
microbiome
9.1 years ago jovel_juan ▴ 30
1
vote
1
reply
1.7k
views
metagenomeSeq error using plotMRheatmap and display() heatmaps and PCA/MDS plots
metagenomseq microbiome
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
1
vote
2
replies
4.6k
views
DESeq2: What is the impact if glm.fit does not converge during rlogTransformation or varianceStabilizingTransformation
deseq2 normalization microbiome
updated 9.6 years ago by 42k • written 9.6 years ago by • 0
1
vote
0
replies
519
views
News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
17 months ago Levi Waldron ★ 1.1k
1
vote
0
replies
890
views
Job: Bioinformatician: NEW YORK CITY - Institute for Data Science and Genomic Technology, Mount Sinai School of Medicine
job bioinformatician systems biology microbiome genomics Job
4.6 years ago supindab ▴ 10
1
vote
3
replies
7.0k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 19 months ago by ▴ 30 • written 3.6 years ago by • 0
1
vote
1
reply
3.0k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
1
vote
1
reply
151
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 20 days ago by ▴ 40 • written 20 days ago by ★ 1.5k
1
vote
1
reply
1.6k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.1 years ago stats134711 • 0
1
vote
1
reply
1.7k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 10
0
votes
2
replies
863
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 4.3 years ago by 42k • written 4.3 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
0
votes
2
replies
746
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 1 day ago by • 0 • written 11 months ago by • 0
0
votes
2
replies
1.2k
views
Question: export edgeR normalised OTU table
microbiome edgeR
3.3 years ago Pozdrawiam • 0
0
votes
0
replies
1.0k
views
News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
3.3 years ago Matthew Ritchie ▴ 1000
0
votes
2
replies
520
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
6 months ago anton.kratz ▴ 60
0
votes
1
reply
919
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
votes
3
replies
1.7k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 21 months ago by 700 • written 21 months ago by • 0
0
votes
1
reply
818
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
votes
2
replies
1.4k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
15 months ago Elif • 0
0
votes
1
reply
587
views
pairwise within sample
DESeq2 microbiome
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
0
votes
1
reply
707
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 20 months ago by 65k • written 20 months ago by • 0
0
votes
1
reply
889
views
Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
0
votes
0
replies
977
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.9 years ago GlycineMax • 0
0
votes
0
replies
381
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
9 months ago Mohamed ▴ 30
0
votes
3
replies
3.4k
views
phyloseq/DESeq gives negative transformed values
Microbiome Normalization Clustering DESeq DESeq2 Microbiome Normalization Clustering DESeq
updated 10.0 years ago by ▴ 130 • written 10.0 years ago by 42k
0
votes
5
replies
3.6k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 7.7 years ago by ▴ 280 • written 7.7 years ago by • 0
0
votes
3
replies
1.4k
views
Correlation analysis
Microbiome HIV Microbiome HIV
updated 12.5 years ago by 21k • written 12.5 years ago by ▴ 20
0
votes
0
replies
3.1k
views
Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
11.6 years ago Dan Tenenbaum ★ 8.2k
0
votes
0
replies
2.6k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
10.8 years ago Luo Weijun ★ 1.6k
0
votes
8
replies
3.3k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 7.8 years ago by ★ 13k • written 10.5 years ago by 42k
0
votes
1
reply
1.2k
views
error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
microbiome
updated 9.5 years ago by ▴ 280 • written 9.5 years ago by • 0
0
votes
5
replies
1.6k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 8.5 years ago by ★ 13k • written 8.5 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
7.8 years ago Daniel Brewer ▴ 100
0
votes
2
replies
1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
7.5 years ago Brian Smith ▴ 120
0
votes
1
reply
1.3k
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 4.1 years ago by • 0 • written 7.4 years ago by • 0
0
votes
3
replies
1.6k
views
Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 7.1 years ago by ★ 13k • written 7.1 years ago by • 0
50 results • Page 1 of 1
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Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning by angelaesper43 • 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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